MolNFT v1 · #161893 · protein
Clpb (dwb and K476C mutant) bound to casein in presence of atpgammas - state kc-2B
6QS8 · Chaperone protein clpb: “Clpb (dwb and K476C mutant) bound to casein in presence of atpgammas - state kc-2B”. Electron microscopy, 3 ligands (AGS, ADP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #161893 on GenesisL1: 3D…
- PDB
- 6QS8
- Type
- protein
- Length
- 3,627 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chaperone protein clpb; Casein
- UniProt
- P63284
- Ligands
- AGS, ADP, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 6 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chaperone protein clpb | protein | 568 | 48% helix, 13% strand | P63284 |
| B | Chaperone protein clpb | protein | 582 | 50% helix, 14% strand | P63284 |
| C | Chaperone protein clpb | protein | 630 | 50% helix, 12% strand | P63284 |
| D, E | Chaperone protein clpb | protein | 625 | 53% helix, 13% strand | P63284 |
| F | Chaperone protein clpb | protein | 573 | 48% helix, 13% strand | P63284 |
| S | Casein | protein | 24 | 0% helix, 29% strand | — |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 10 copies · chains A, F, B, C, D, E
- ADP · Adenosine-5'-diphosphate · ligand · chains E, F
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1131 | 0.86 | 0.88 | 126 | AGS, MG |
| 2 | 1143 | 0.86 | 0.87 | 125 | AGS, MG |
| 3 | 1079 | 0.85 | 0.86 | 107 | AGS, MG |
| 4 | 840 | 0.84 | 0.86 | 65 | AGS |
| 5 | 678 | 0.83 | 0.87 | 78 | AGS, MG |
Interfaces
15 interfaces between chains.
- B–C · 4716 Ų buried · 86 hydrogen bonds · protein-protein
- C–D · 4695 Ų buried · 84 hydrogen bonds · protein-protein
- D–E · 4552 Ų buried · 76 hydrogen bonds · protein-protein
- A–B · 3782 Ų buried · 63 hydrogen bonds · protein-protein
- E–F · 2385 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6QS8 · ClpB (DWB and K476C mutant) bound to casein in presence of ATPgammaS - state KC-2B · the same entry in another collection · chain S against S, TM-score 1.00
- P63284 · AlphaFold monomer V2.0 prediction for chaperone protein clpb (P63284) · a predicted model of the same protein · chain F against A, TM-score 0.89
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P63284
- Elsewhere: RCSB PDB 6QS8 · PDBe 6QS8 · UniProt P63284
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